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Bioinformatics Glossary Based Database of Biological Databases: DBD J Biochem Tech (2009) 1(3):88-90 ISSN: 0974-2328 Bioinformatics glossary based Database of Biological Databases: DBD Siva Kiran RR, Setty MVN, Hanumatha Rao G* Received: 16 May 2009 / Received in revised form: 17 May 2009, Accepted: 18 May 2009, Published online: 6 June 2009 © Sevas Educational Society 2008 Abstract Database of Biological/Bioinformatics Databases (DBD) is a Databases of Biological Databases such as DOD – Database of collection of 1669 databases and online resources collected from Databases (http://www.progenebio.in/DoD/DoD.htm), MetaBase - NAR Database Summary Papers (http://www.oxfordjournals.org The Database of Biological Database (http://biodatabase.org) and /nar/database/a/) & Internet search engines. The database has been The Molecular Biology Database Collection – Updates developed based on 437 keywords (Glossary) available in (Baxevanis 2000), published annually by journal entitled “Nucleic http://falcon.roswellpark.org/labweb/glossary.html. Keywords with Acids Research” help researchers to identify and correlate important their relevant databases are arranged in alphabetic order which queries beside providing a common platform for various molecular enables quick accession of databases by researchers. Database biology databases. Databases in DOD, Metabase & others have been description provides brief information about the database with a link grouped into categories as conceived by the respective authors. For to main web page. DBD is available online and can be accessed at instance, DOD has grouped 719 databases into 14 major categories http://www.biodbs.info. (Galperin 2005) while Metabase has grouped 1119 databases into 21 categories. Keywords: Databases, biological databases, bioinformatics databases, bioinformatics glossary The uniqueness of the present DBD is the alphabetic listing of all databases based on technical terms (keywords) viz. Introduction http://falcon.roswellpark.org/labweb/glossary.html. This facilitates Molecular biology has witnessed an information explosion in the very quick access to the desired databases. last two decades as a consequence of development of rapid DNA sequencing techniques. The concomitant progress in computer based Figure 1: Structure of DBD (Database of Biological Databases) technologies has enabled molecular biologists in general and bioinformatists in particular to cope with this information deluge. Information from various sources explicitly presented in the form of biological databases is generally maintained by many institutions. They vary widely in their content, format and access method [Kihler 2004]. Biological data are being deposited in a database and the need for data analysis has made molecular biology databases vital tools for research. Although several databases are reported in literature, many researchers are not aware of their availability and these databases were not effectively utilized (Ajay Babu et al. 2005). R.R. Siva Kiran, MVN Setty Department of Biotechnology, M S Ramaiah Institute of Technology, Bangalore – 560054, India Steps involved in construction of DBD (Figure 1) G. Hanumatha Rao* Center for Biotechnology, Department of Chemical Engineering, • Extraction of suitable keywords from bioinformatics glossary University College of Engineering, Andhra University, website http://falcon.roswellpark.org/labweb/glossary.html. • Typing the keyword along with the suffix “Database” in Visakhapatnam-530 003, India. popular search engines like http://www.google.com, *Tel: 0091 891 284 4878; Fax: 0091 891 274 7969 http://www.yahoo.com etc. Email: [email protected] J Biochem Tech (2009) 1(3):88-90 ISSN: 0974-2328 Table 1: Alphabetical listing of the number of keywords with the total number of databases linked to DBD (Database of Biological Database) Total Total number Alphabets Some major keywords with total number of database linked to DBD keywords of databases A 16 64 Alignment – 8, Alternative Splicing – 22, Annotation – 12, Agricultural – 4 B 20 68 Bacterial – 8, Bacillus – 6, Binding – 6, Biochemical Pathway – 9, Biological databases listing - 11 C 48 88 Caenorhabditis elegans – 5, Cancer – 14, Chromosome – 9, Cytogenetics – 3, Cluster - 4 D 33 76 Disease – 12, Domain – 9, Drosophila -15, DNA – 18 E 25 86 E.coli – 14, Enzyme – 16, Eukaryotic – 8, EST – 11, Expression databases – 5, EBI – 3, Evolution - 3 F 12 19 Fish – 3, Fly -3, Functional Genomics - 4 G 15 77 Genome – 38, Gene & Gene Expression – 16, Genetics – 7, Germ - 6 H 25 93 HIV – 21, Homologous & Homology – 17, Human – 18, Haemophilus – 3, Higher taxon - 5 I 23 56 Inhibitor - 10, Intron – 6, Isotope - 4 J Nil Nil Nil K 4 4 Kinases – 1, KEGG - 1 L 9 32 Ligand – 23, Liver proteome - 1 M 41 258 Motif - 10, Metabolic Pathway - 11, Microarray - 22, Microbial - 15, Mitochondrial - 25, Mouse - 30, Mutation - 40 N 11 34 NMR - 5, Nucleic - 4, Nucleotide - 6 O 11 38 Oligo – 38, Organelles - 7, Ortholog - 9 Parasite - 10, Pathway - 12, PCR - 8, Peptide - 34, Phenotype - 9, Plant - 5, Plasmid - 10, Primer - 10, Probe - 13, Promoter P 52 297 – 15, Protease - 12, Protein - 53, Proteome - 18 Q 3 11 QSAR - 6, Quantitative trait loci - 4 R 19 113 Radiation hybrid - 6, Rat - 20, Retrovirus - 5, RNA - 39, Ribosomal – 7, Rice - 17 S 34 132 Sanger - 4, Sequence - 44, Signal Transduction - 8, SNP - 16, Species - 5, Structure - 13, Synapse - 3 T 19 47 Taxonomy - 3, Transcript - 5, tRNA - 3, Transgenic - 3, Tumor - 9, Tree - 3 U 3 7 Unigene - 4, UniProt - 2 V 5 31 Variation - 9, Virus - 16, Vector - 4 W 3 4 Worm - 2 X 3 4 X chromosome - 2, Xenopus laevis - 1 Y 2 25 Yeast - 23 Z 1 5 Zea mays - 5 90 J Biochem Tech (2009) 1(3):88-90 For example genome keyword can be typed as “Genome Kïhler J (2004) Integration of life science databases. DDT: Database” in search engine. BIOSILICO 2:61-69 • Collection of databases from “NAR Database Summary Ajay BP, Radha B, Lakshmi VV, Rao NG (2005) DoD: Database of Papers-Alphabetical List” available in the website Databases - updated molecular biology databases. In Silico (http://www.oxfordjournals.org/nar/database/a/) Biology 5:0054 </isb/2005/05/0054/> • Listing all databases in tables along with suitable keywords. Baxevanis AD (2000) The Molecular Biology Database Collection: an online compilation of relevant database resources. Nuc Acids Figure 2: Screenshot of Database of Biological Databases (DBD) Res 28(1):1-7 Galperin MY (2005) The Molecular Biology Database Collection: 2005 update Nuc Acids Res. doi:10.1093/nar/gki139 Features of DBD: All keywords are arranged in alphabetic order as shown in Figure 2. Databases are listed along with the keywords (Table 1). The description of database has been reduced so as to accommodate more databases with keywords. Websites pertaining to bioinformatics keywords like Alignment, SQL, Base Pair, Blast, Biotechnology etc are also listed for helping researchers to reduce their time in finding suitable information. Tutorial websites are also listed along with databases. The listed databases or tutorial websites are based solely on the display of the relevant websites present in search engines. Conclusion The primary aim of DBD is to provide an easy access to a number of databases, tutorial websites etc. based on keywords. Brief description about the databases and keyword helps the users to know the contents of the database, their respective keywords and database links. The DBD shall be updated periodically for the benefit of researchers and more bioinformatics/biology keywords will also be added to the database. We are confident, that the DBD will be highly useful tool in the hands of molecular biologists and bioinformaticians. Acknowledgement The authors thank Rajesh K of Department of Pharmacy, Andhra University, India, Rohit MD, Mubashir HM, Yomeen RM, of Dept. of Biotechnology, MS Ramaiah Institute of Technology, Bangalore, India and Sangeeta Uranakar, Naganandini G and Usha D of University Visweswaraiah College of Engineering, K R Circle, Bangalore, India for their contributions in the development of this database. References Attwood TK, Parry-Smith DJ (2000) Introduction to Bioinformatics, 1st edn. Prentice Hall, UK .
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